Home › Studies › PRJDB10829

PRJDB10829 DRP008216

Gut metagenome in Japanese CRC and postoperative patients

Generic sample from human gut metagenome

112 fecal metagenome samples from Japanese colonoscopy patients at a national cancer research center, including colorectal cancer (CRC) and postoperative cases, studied using a case-control design. machine-written summary

112 samples · 112 runs · JP · Age unknown · 2022 · 6.43 Gbp / sample · cohort Surgical Treatment for Colorectal Cancer Partially

ENA BioProject Sample sheet Registry Download Flag an issue

Sources

✓Sequence archive 560✓Abstract / description 336○Full text✓Supplementary tables 424–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	560 sample values (collection date, country, latitude, longitude, subject id)
✓ Abstract / description	336 sample values (health condition, health condition detail, location site)
○ Full text	read; no usable statement or table · PMC9040882
✓ Supplementary tables	424 sample values (age, bmi, intervention, sex, timepoint)
– External resources	not covered by the external resources we ingest
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Samples at a glance

1 sampling locations · 1 country

Age

unknown68

adult32

elderly12

Condition

colorectal_cancer112

Sex

male67

female45

Country

JP112

Body site

primary112

Collected 2015–2019

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal — not resolved

44 of 68 people sampled more than once (88 samples; median 2, up to 2 per person). Schedule stated by the source: “Pre-surgery and approximately 1 year post-surgery (two time points per patient)” (time origin: surgery); stated follow-up 12 mo.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 13.2%Phocaeicola 13.0%Prevotella 7.2%Roseburia 3.9%Parabacteroides 3.7%Faecalibacterium 3.6%Alistipes 2.9%Bifidobacterium 2.8%Lachnospira 2.5%Mediterraneibacter 1.9%Enterocloster 1.9%Blautia_A 1.8%not assigned to a genus 6.0%other genera 35.5%

Genera, mean relative abundance over 104 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R2	R4
age_category	44	39%
country	112	100%	112
health_condition	112	100%			112
subject_id	112	100%	112
collection_date	112	100%	112
detailed_location	112	100%
health_condition_detail	112	100%			112
intervention	112	100%		112
latitude	112	100%	112
location_site	112	100%			112
longitude	112	100%	112
sex	112	100%		112
timepoint_label	112	100%		112
age_at_collection_days	44	39%		44
bmi	44	39%		44

Papers (1)

Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. 2022 PMID 35311577 PMC9040882 own_data

Details

Archive description

Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains CRC and postoperative patients.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.

host run.host_tax_id · “9606”
body site run.scientific_name · “human gut metagenome”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMD00260087	age_at_collection_days	26663.0	R2	0.80	paper.supp.msystems.00018-22-st001.xlsx[Table_S1-4!Age (Pre, years)]	10882: 73
SAMD00260087	bmi	19.82	R2	0.80	paper.supp.msystems.00018-22-st001.xlsx[Table_S1-4!BMI (Pre, kg/m2)]	10882: 19.81784449
SAMD00260019	collection_date	2015	R1	0.90	biosample.attribute:collection_date	2015
SAMD00260019	country	JP	R1	0.90	sample.attr.geo_loc_name	Japan
SAMD00260019	health_condition	colorectal_cancer	R4	0.50	paper.abstract	we collected 170 fecal samples from 85 CRC patients pre- and approximately 1 year postsurgery
SAMD00260019	health_condition_detail	CRC patients pre- and approximately 1 year postsurgery	R4	0.50	paper.abstract	we collected 170 fecal samples from 85 CRC patients pre- and approximately 1 year postsurgery
SAMD00260019	intervention	other_intervention	R2	0.80	paper.supp.msystems.00018-22-st001.xlsx[Table_S1-4!Methods]	10140.1: ESD
SAMD00260019	latitude	35.6600	R1	0.90	biosample.attribute:lat_lon	35.66 N 139.76 E
SAMD00260019	location_site	National Cancer Research Center	R4	0.45	ena.study_description	colonoscopy at National Cancer Research Center
SAMD00260019	longitude	139.7600	R1	0.90	biosample.attribute:lat_lon	35.66 N 139.76 E
SAMD00260019	sex	female	R2	0.80	paper.supp.msystems.00018-22-st001.xlsx[Table_S1-4!Gender]	10140.1: F
SAMD00260019	subject_id	10140	R1	0.70	sample.name_rule:attr_sample_name	10140.1
SAMD00260130	subject_id	11274	R1	0.70	sample.name_rule:sample_title	human feces_11274
SAMD00260019	timepoint_label	Post	R2	0.80	paper.supp.msystems.00018-22-st001.xlsx[Table_S1-4!Timepoint (ID column)]	10140.1: Post

Sequencing

112 runs over 112 samples · mean 6.10 Gbp per run (median 6.43 Gbp, total 683.41 Gbp; 112 runs with a base count) · layout PAIRED 112 · platform ILLUMINA 112 · models Illumina HiSeq 2500 (112) · 93% of runs with a Sandpiper profile · first public 2022-02-23

Authors (0)

No author record.

Downloads

PRJDB10829.csv.gz (4.7 KB) · parquet (76.7 KB) — all 112 samples, every field with route and confidence · PRJDB10829_determinations.csv.gz (13.3 KB) — 1,320 evidence rows

Samples (112 · every field this project has values for · hover a cell for its source)

Loading the sample table…